Most of the time, it's because the evaporated metal coats the polymer sidewalls. To do a better lift-off, it's best using a bilayer design where you have a higher molecular weight polymer on top of a lower molecular weight polymer, as shown in the figure below.

When you expose the bilayer with ebeam, an undercut is formed. Due to the undercut, you avoid coating the sidewall of the resist when you evaporate metal. Lift-off then becomes a breeze!

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